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Protein

Clarin-1

Gene

Clrn1

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: -Experimental evidence at transcript leveli

Functioni

May have a role in the excitatory ribbon synapse junctions between hair cells and cochlear ganglion cells and presumably also in analogous synapses within the retina.1 Publication

GO - Biological processi

Keywordsi

Biological processHearing, Sensory transduction, Vision

Names & Taxonomyi

Protein namesi
Recommended name:
Clarin-1
Alternative name(s):
Usher syndrome type-3 protein homolog
Gene namesi
Name:Clrn1
Synonyms:Ush3a
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaMyomorphaMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Chromosome 3

Organism-specific databases

MGIiMGI:2388124 Clrn1

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Topology

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Transmembranei8 – 28HelicalSequence analysisAdd BLAST21
Transmembranei101 – 121HelicalSequence analysisAdd BLAST21
Transmembranei135 – 155HelicalSequence analysisAdd BLAST21
Transmembranei186 – 206HelicalSequence analysisAdd BLAST21

Keywords - Cellular componenti

Cell membrane, Membrane

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002746951 – 232Clarin-1Add BLAST232

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Glycosylationi48N-linked (GlcNAc...) asparagineSequence analysis1
Glycosylationi184N-linked (GlcNAc...) asparagineSequence analysis1

Keywords - PTMi

Glycoprotein

Proteomic databases

PRIDEiQ8K445

PTM databases

iPTMnetiQ8K445
PhosphoSitePlusiQ8K445

Expressioni

Gene expression databases

BgeeiENSMUSG00000043850 Expressed in 37 organ(s), highest expression level in ear vesicle
CleanExiMM_CLRN1
ExpressionAtlasiQ8K445 baseline and differential
GenevisibleiQ8K445 MM

Structurei

3D structure databases

ProteinModelPortaliQ8K445
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the clarin family.Curated

Keywords - Domaini

Transmembrane, Transmembrane helix

Phylogenomic databases

GeneTreeiENSGT00850000132319
HOGENOMiHOG000060265
HOVERGENiHBG061269
InParanoidiQ8K445
OMAiAYKTQSE
OrthoDBiEOG091G0H1F
PhylomeDBiQ8K445
TreeFamiTF331875

Family and domain databases

InterProiView protein in InterPro
IPR026748 Clarin
PANTHERiPTHR31548 PTHR31548, 1 hit

Sequences (2+)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

This entry has 2 described isoforms and 1 potential isoform that is computationally mapped.Show allAlign All

Isoform 1 (identifier: Q8K445-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide
        10         20         30         40         50
MPSQQKKIIF CMAGVLSFLC ALGVVTAVGT PLWVKATILC KTGALLVNAS
60 70 80 90 100
GKELDKFMGE MQYGLFHGEG VRQCGLGARP FRFSFFPDLV QAIPVSIHIN
110 120 130 140 150
IILFSMILVV LTMVGTAFFM YNAFGKPFET LHGPLGLYLV SFISGSCGCL
160 170 180 190 200
VMILFASEVK VHRLSEKIAN FKEGTYAYRT QNENYTTSFW VVFICFFVHF
210 220 230
LNGLLIRLAG FQFPFTKSKE TETTNVASDL MY
Length:232
Mass (Da):25,804
Last modified:October 1, 2002 - v1
Checksum:i6B782144A070DB3F
GO
Isoform 2 (identifier: Q8K445-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     84-85: SF → SSRSMKERYSLYEDKGETAV

Show »
Length:250
Mass (Da):27,888
Checksum:i36BBD93F66F7DA7A
GO

Computationally mapped potential isoform sequencesi

There is 1 potential isoform mapped to this entry.BLASTAlignShow allAdd to basket
EntryEntry nameProtein names
Gene namesLengthAnnotation
Q8K444Q8K444_MOUSE
Clarin-1
Clrn1 Ush3a, mCG_66391
172Annotation score:

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_02287084 – 85SF → SSRSMKERYSLYEDKGETAV in isoform 2. 1 Publication2

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF495718 mRNA Translation: AAM88775.1
AF495719 mRNA Translation: AAM88776.1
CCDSiCCDS38438.1 [Q8K445-1]
CCDS38439.1 [Q8K445-2]
RefSeqiNP_700433.1, NM_153384.3 [Q8K445-2]
NP_700434.1, NM_153385.3 [Q8K445-1]
NP_700435.1, NM_153386.3
UniGeneiMm.131502

Genome annotation databases

EnsembliENSMUST00000051408; ENSMUSP00000051738; ENSMUSG00000043850 [Q8K445-1]
ENSMUST00000055636; ENSMUSP00000052254; ENSMUSG00000043850 [Q8K445-2]
GeneIDi229320
KEGGimmu:229320
UCSCiuc008pid.2 mouse [Q8K445-2]
uc008pie.2 mouse [Q8K445-1]

Keywords - Coding sequence diversityi

Alternative splicing

Similar proteinsi

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF495718 mRNA Translation: AAM88775.1
AF495719 mRNA Translation: AAM88776.1
CCDSiCCDS38438.1 [Q8K445-1]
CCDS38439.1 [Q8K445-2]
RefSeqiNP_700433.1, NM_153384.3 [Q8K445-2]
NP_700434.1, NM_153385.3 [Q8K445-1]
NP_700435.1, NM_153386.3
UniGeneiMm.131502

3D structure databases

ProteinModelPortaliQ8K445
ModBaseiSearch...
MobiDBiSearch...

PTM databases

iPTMnetiQ8K445
PhosphoSitePlusiQ8K445

Proteomic databases

PRIDEiQ8K445

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSMUST00000051408; ENSMUSP00000051738; ENSMUSG00000043850 [Q8K445-1]
ENSMUST00000055636; ENSMUSP00000052254; ENSMUSG00000043850 [Q8K445-2]
GeneIDi229320
KEGGimmu:229320
UCSCiuc008pid.2 mouse [Q8K445-2]
uc008pie.2 mouse [Q8K445-1]

Organism-specific databases

CTDi7401
MGIiMGI:2388124 Clrn1

Phylogenomic databases

GeneTreeiENSGT00850000132319
HOGENOMiHOG000060265
HOVERGENiHBG061269
InParanoidiQ8K445
OMAiAYKTQSE
OrthoDBiEOG091G0H1F
PhylomeDBiQ8K445
TreeFamiTF331875

Miscellaneous databases

PROiPR:Q8K445
SOURCEiSearch...

Gene expression databases

BgeeiENSMUSG00000043850 Expressed in 37 organ(s), highest expression level in ear vesicle
CleanExiMM_CLRN1
ExpressionAtlasiQ8K445 baseline and differential
GenevisibleiQ8K445 MM

Family and domain databases

InterProiView protein in InterPro
IPR026748 Clarin
PANTHERiPTHR31548 PTHR31548, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiCLRN1_MOUSE
AccessioniPrimary (citable) accession number: Q8K445
Secondary accession number(s): Q8K446
Entry historyiIntegrated into UniProtKB/Swiss-Prot: February 6, 2007
Last sequence update: October 1, 2002
Last modified: November 7, 2018
This is version 89 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
  2. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
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Main funding by: National Institutes of Health

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